Mass Effect: Guardians of Evolution
by BXA
Summary: It has been 6 years since The Shepard disappeared with his Guardians but when one of them is suddenly found dormant on Eden Prime, a young Captain with the Alliance is put in charge of a mission, which she suspects will only bring about old horrors. Friends of Shepard rally to help her but what is one to do if the real threat is within? Multiple POV's. Future pairings.
1. An unsettling discovery

**_All hail The Shepard  
For he has come to our salvation  
He has brought back his Guardians  
To bless us anew_**

* * *

**Prologue**

"Zeph?"

Mu'Ral slowly took a few steps forward; feeling the dread of the sight he was expecting behind the grassy hill, rapidly overtake him with each hesitant step. As he walked around the small mound, a plain of grass lay silent in front of him painted red with blood and covered with human corpses scattered against the ground and surrounding rocks, but the lone Geth that was his stood completely motionless and did not turn at the sound of his voice. He called the Geth's name again, this time louder and more insistent. The Geth slowly tilted its neck and seemed to ponder the silence of the small valley. "Zeph, get in the vehicle now!" Mu'Ral commanded frantically, but the Geth remained hesitant.

A small whimper suddenly emanated from a bloodied body beside Mu'Ral and his eyes met the face of a woman sprawled against a rock and cringing in pain at the gaping hole in her chest. Mu'Ral kneeled before her with trembling hands. _Should I give her peace?_ A bird cried somewhere in the distance and he heard the slow resounding steps of his Geth approaching. He stared at the face of the woman and watched the color of her skin slowly turning more and more sallow, but he remained undecided. He summoned up his courage and produced a small blade from his pocket, when the deafening sound of a gunshot caused a small group of birds to immediately take to the sky from a tree beside the hill. An instant sigh of death escaped the woman's lips and Mu'Ral slowly lifted his head.

"I'm sorry, Mu'ral. They attacked us." Mu'Ral stared at the Geth for a moment before his eyes turned to the dead woman. The small S-shaped pendant around her neck gleamed in the sunlight and Mu'Ral stole another remorseful glance at her before he clenched his jaw and rose from the ground.

"Come on Zeph, let's return to the settlement."

* * *

**SSV Yorktown year 2195**

"Coming up on the Charon relay, Captain"

The Captain narrowed her eyes to get a better look at the view of the giant structure directly ahead, floating motionlessly in the black void. As the _Yorktown _flew in closer the familiar blue surges of energy reached forward to take hold of the ship and the Captain braced herself for the unmistakable sense of vertigo that would imminently follow. She closed her eyes and let herself hover for a moment above the floor of the bridge while the dominant blinding light seemed to tear her to a sub-atomic level, only to reassemble her almost instantly after. She uttered a small sigh of relief as she opened her eyes again and felt the firm ground of the bridge underneath her boots. She couldn't count how many times she had gone through a similar exercise, but she suspected she would never quite get used to it and always felt a slight sense of dread at the anticipation of passing through a relay.

It had been almost 6 years since she had last seen the large sentinel Reaper hovering over the Charon Relay but she always insisted on being present on the bridge whenever a vessel, on which she was either the commanding officer or a passenger, would approach a mass relay. She wanted to make absolutely sure that the assigned Reaper was gone before she would allow herself to release the air she had deliberately kept in her lungs from the ever-present, nagging suspicion that the Reaper had somehow lingered.

She watched the star-sprinkled vacuum of the Exodus Cluster and peered through all the windows on the bridge searching for the planet for which the ship was destined. Her head automatically turned to the pilot when he extended his hand to his right. "There, Eden Prime" he said. Her eyes followed and settled on the approaching human colony while she felt an intense uneasiness emerge and quickly spread from the pit of her stomach. She could feel her features twisting into an involuntary grimace at the thought of her business there and forced herself to stare blankly at one of the pilots consoles while she inhaled deeply through her nostrils.

"Are you okay, Captain?"

She turned and saw the worried expression on the face of the young Marine behind her and quickly gave him a nod before she let her hands rest against the pilot's seat and resettled her eyes on the planet ahead. _Am I the only one who's nervous about this?_

"We should be grateful. Maybe this means he's come back"

The voice belonged to her Lieutenant-Commander and she heard the British woman mutter a quick prayer and knew she was fingering the small pendant around her neck even though the LC was not within her field of vision. _It's a little late for prayers_. She wondered what the rest of the galaxy would think if when it was revealed what the colonists had found on Eden Prime and decided that most of them would probably shed tears of joy. The Captain knew however that she was not one of them.

Eden Prime came closer into view and the Captain rolled her neck before she turned and addressed her soldiers. "We'll be landing soon. Get ready" she commanded and allowed herself a deep breath before she turned in the direction of the air-lock.

* * *

**Nos Astra, Illium, Crescent Nebula**

"She.. lan.. so… Eden Pri…"

The wavy lines and constant shimmer on the holo-screen against the window made the asari in the dark office involuntarily blink from the persistent strain on her eyes. Her assistant had already been set to work at clearing up the interference, but her patience was stretching thin and she knew the Captain was only minutes away from her destination.

"What is the latest report from Eden Prime?" Liara T'Soni asked her contact.

"Guardi… silent there's no act…"

Liara stared at Glyph for a moment to get a better notion of how far her drone was in its efforts to clear the image. The little drone rotated energetically in the air and emitted small repetitive buzzes as if sending out a physical manifestation of its hard work. Liara waited patiently for another few seconds before she accepted that the drone's efforts were evidently futile and then paused the transmission for a moment to address it.

"Leave it, Glyph"

The drone immediately hovered over to her desk and fell silent.

Liara resumed he transmission and turned her attention to the holo-screen. "Thank you Brazz. I'll be in touch later if necessary." She pressed a button on her omni-tool to end the broadcast and turned to watch the view of the trading floor of Nos Astra spaceport, before she hesitantly raised a hand to touch the S-shaped pendant around her neck.

_"I love you, Liara, and one day I'll come back"_

Her eyes threatened to well up again, as they had so many times in the past 6 years at the memory of those last words from her lover and she forced her eye-lids closed as if to both suppress and summon the image of the last time she had seen John, when he had suddenly appeared as a white shimmer in her apartment. She had reached out and tried to kiss him, but the warmth of his lips was denied her and she had felt only tepid air on her face instead of the familiar tickling sensation from the friction against the brown bristles on his cheeks and upper lip. She had closed her eyes for only an instant, but when she had opened them again he had been gone and the room had been dark. Her heart had slowly shattered in her chest at the realization that John was leaving the galaxy, but she had later acknowledged a small sense of relief which she had tried to simultaneously suppress along with her instant longing for his return.

Thousands of the Reapers had been sacrificed to reconstruct the mass relay cores, and Liara still remembered the large Reaper which had found the Normandy and transported it back to the Citadel. They had all been frozen with terror at the sight before Joker had found his voice and ordered EDI to fire at it, but the Reaper had quickly sent out a transmission to their AI companion stating that it was John's wish that they be saved and transported back to civilization. Liara had later learned that other Guardians had been given the task of flying in supplies to the different races trapped on Earth and other planets, effectively stifling inevitable anarchy caused by frenzied, helpless organics to ensure their own survival. The rebuilding had not been without casualties, but they had thankfully been acceptable given the circumstances and Liara often wondered how long it would have taken for the galaxy to rebuild itself without the help of the Guardians, and estimated that it would probably not have occurred within her lifetime. For this she was immensely thankful even if it had meant that John was no longer John, but rather the overseer of the reconstruction of a devastated galaxy.

Shepard had addressed the people of the galaxy through their omni-tools only minutes after he had activated the catalyst and ensured them that he would help in whatever way he could to restore what they had lost. He had sometimes sent Liara messages afterwards, mostly words of reassurance and love, but she had never found a way to contact him back and the only time she had ever seen him since was that one night when he had appeared in her apartment. She had been sound asleep, but then awoken by an ominous voice which had firmly, but gently, told her to wake. His visit had been short and she had instantly known before he had even spoken that he would leave and probably not come back, despite his promises of the contrary.

She watched a few asari kneeling before a statue to the left of a trading terminal and let an image of Shepard linger in her mind. _Are you coming back to me now John?_ She had not dared hope that he would actually return and she had begun to wonder progressively more over the years if she in fact truly wanted him to. He was no longer the same charismatic human male she fallen in love with, but rather a monolithic, incomprehensible entity whom had admittedly made her feel unworthy of his continued devotion to her. She was not the only one who loved him anymore; people from across the galaxy had begun to worship Shepard. They called him a prophet and wore the S-shaped symbol as a token of their faith and everywhere around the galaxy statues of him and his Guardians were still being made in his honor.

The sudden presence of a Guardian in the Exodus cluster filled Liara with equal amounts of thrill and anxiety, but she had decided to keep her emotions in check until it had been confirmed why a Guardian had suddenly returned to the Milky Way after having been absent along with its kin for almost 6 years. Her thoughts went to the Captain currently on Eden Prime, and she fingered the pendant vigorously as she watched the asari mouthing a prayer before the statue.

* * *

**Vancouver, Earth, Sol System**

Kaidan Alenko felt his heart beating steadily faster as he proceeded down the small corridor in quick strides, offering small nods to the reverse traffic of saluting young men and women of the Systems Alliance. The discussion he was about to have with his superior officer was one he had dreaded for hours, and he was yet to come up with a viable explanation, nor had he been able to produce an even remotely satisfying plan for dealing with the sudden presence of a dormant Guardian. The Alliance-officer who had forwarded the news had stammered the words out with an expression of sheer terror on his face, and Kaidan had for once been unable to give a consoling response, instead offering a simple nod of affirmation before he had dismissed the soldier with a wave of his slightly trembling hand. Discussing the news in person with his superior officer was a conscious choice, since he needed the assurance of complete privacy without constantly having to carefully choose his words from the fear of their conversation being intercepted by unwanted parties, such as the very keen hackers of the Shepardist-movement.

He paused for a moment outside the door and allowed a memory to quickly surface. It was the last time he had spoken to John in London and he remembered the relentless pounding in his chest, which he had been confident that Shepard had noticed, even if he had kept his words composed and his expression calm.

After having allowed himself a deep quiet breath, he carefully opened the door and hesitantly peered inside, feeling like a child hoping for the absence of his parents, so he could raid the refrigerator in peace.

"Don't hover, General!"

The authoritative voice of Admiral Hackett had never been a favorite of Kaidan's but the Admiral was nevertheless his commanding officer, and the one who had entrusted Kaidan with the responsibilities of being a General with the Alliance. Permitting himself a moment to successfully shake an unwanted feeling of nervousness, Kaidan approached the Admiral's desk and turned his stance firm and rigid.

"Sir!" Kaidan said with a salute.

Hackett beckoned his General to have a seat opposite him, before he took a long gulp from a coffee-cup with the Alliance-logo.

"Well, what's the latest report from your Captain?" Hackett asked somewhat impatiently.

Kaidan rubbed his hands nervously between his legs for a moment, being careful to keep the gesture hidden from the Admiral.

"They're on their way, sir. I've asked that the Captain only take a small group with her. The population of the colony needs to feel secure that we consider this a strange, but unthreatening… thing"

Admiral Hackett leaned back in his chair and fingered the scar over his mouth. "What are your expectations, General? Will it wake up you think?"

"I think it would have awoken by now, if that was the case, sir. I've sent the Captain to have a look before we haul it back… just in case" His words sounded strangely small in his ears, and he silently scolded himself for not having the courage to produce a confident response.

"Shepard has been gone for six years. Why is he suddenly sending a Guardian back now? And one who is inactive?" Hackett asked.

Kaidan sensed the presence of anxiety in his CO's voice and it did nothing to stifle his own growing apprehensions. "I have no idea, Admiral" Kaidan admitted. "But I think we ought to consider the possibility that the Guardian will wake, and it might be hostile if it does"

Despite Kaidan's conviction that both men had already come to terms with this possibility, the Admiral's large office immediately filled with an ominous tension, and Kaidan found himself studying the weather-beaten face of that man, who had sacrificed so many lives during the war in a desperate effort to buy Commander Shepard time to bring about the final solution.

The Admiral took another sip of his coffee, and Kaidan's eyes automatically went to the logo on the white porcelain. _Are we truly ready for this?_

"Are you putting the Captain in charge if our worst expectations come true?"

The Admirals words sounded somehow distant in Kaidan's ears, as if spoken from somewhere outside the room.

"Yes, sir" Kaidan answered, while he suppressed an urge to swallow something. He in fact had no real choice in the matter. _Quinn, please survive this!_


	2. The charitable eye of The Shepard

**The Citadel, Serpent Nebula**

The tall balding man walked at a brisk pace down the long corridor of the presidium, stealing glances left and right at the wonderful multicultural population of the Citadel. A few asari eyed him nervously from their position next to a large display but Erik Nielsen, leader of the Shepardist-movement, granted them his most courteous nod while he tried to stifle the headache which was rapidly threatening to materialize somewhere in the back of his skull. The asari immediately averted their eyes at his gesture however, and Nielsen emitted a small sigh of exasperation at the evident display of distrust from his fellow beloved organics. _Why can't they understand that I only want to protect them? _He proceeded to the elevator and quickly pressed the button to the embassies, before he rolled his neck and closed his eyes to focus. After a moment a galaxy news network correspondent broke the silence in a soothing voice.

**Today it was revealed that another attack has occurred on a processing lab on Zanethu in the Hourglass Nebula. It has still not been confirmed who was behind the attack, but the lead scientist at the lab is apparently inclined to believe that an extreme group of Shepardists orchestrated the assault and urges the people of the galaxy to rethink their affiliations with the group. Our head correspondent, Khalisah Bint Sinan al-Jilani, announces that she will follow up on the matter and intends to request another interview with the leader of the Shepardists, the Earth-born Erik Nielsen. We will of course feature the interview as soon as it has taken place.**

Nielsen stared at the small speaker in the upper-right corner of the elevator with a contemptuous smile. _Thanks for the heads-up. _Westerlund news had always been packed with slow-witted individuals and Nielsen made a mental note to tell his assistant to immediately reject any proposition from this ambitious head correspondent with whom he had unfortunately become intimately acquainted over the past few years.

The elevator doors opened and Nielsen stepped out in the lounge area before he resolutely turned in the direction of the stairs to his right. Some humans nodded at him with approving smiles and he quickly drew the S-symbol in the air with a finger and watched them become visibly awed at the attention he granted them. He greeted the guards outside the door to the human embassy and allowed himself to be scanned by their omni-tools before one of the large turian C-Sec officers pushed the green entry-button and beckoned him proceed.

Inside the human Councilor Dominic Ososba glanced up from his desk and Nielsen thought the Councilor looked already somewhat downcast at his presence, but ignored his own observation and approached the Councilor's desk.

"Councilor" Nielsen said with a curt nod.

The Councilor nodded in greeting and beckoned Nielsen take a seat opposite him. "Nielsen. I suppose you have come to urge the Council to resume its ban on the development of AI's?"

Nielsen recognized weariness in the Councilor's tone. It was not the first time he had addressed the Council with this plea but he was determined to continue until he achieved his goal of an AI-free galaxy, and if that meant paying unannounced visits to the human Councilor with the risk of one day being denied access, then that was the course he must take. "Yes Councilor. I will spare you my usual arguments and only present a new one. The Geth have started to make AI's of their own"

The Councilor looked startled for a moment, before his expression then turned distinctly suspicious. "And how is it that the Council is not aware of this?"

Nielsen curled his full lips into a smile. This statement had in fact not been confirmed, but he was admittedly turning somewhat desperate and the person from whom he had received this intelligence was not without some credibility. "I doubt the Council will know everything that's happening in the galaxy and the quarians have always seemed determined to exempt themselves from the intergalactic community"

The Councilor's blue eyes immediately flared with resentment. "I see. I suppose you have learned this from the last time your hoards attacked the Geth?" he asked with obvious contempt.

Nielsen's smile turned deliberately sympathetic. "I assure you once again that I had nothing to do with those attacks" he replied calmly.

The Councilor did not seem convinced, but Nielsen knew they had no proof that this indictment and Osoba's expression then seemed to soften somewhat, since they both knew that proceeding with a discussion of this subject was a waste of time.

"The galaxy lost billions of lives Nielsen, but it is now repopulating and we need to meet up with demand. New intelligent machines can help us achieve that goal much faster than the backbreaking labor from already tried organics" the Councilor argued compassionately.

Nielsen shook his head lightly with impatience. "By making new abominations that could become self-aware? We must keep ourselves from such folly, Councilor. We must only create VI's and only at a limited function. The machines must not be allowed to think for themselves"

"VI's cannot help with the labor. Their design is limited to assistance of processing data. We need physical instruments to help" the Councilor retorted.

"Then make machines with VI programming to help other tech do the job more easily" Nielsen shot back.

The Councilor released a low sigh. "We need smarter machines than that. The Geth stayed on Rannoch to help resettle the quarians homeworld, and they co-exist with them peacefully to this day. It can be done, Nielsen" the Councilor assured.

Nielsen resisted an urge to roll his eyes. He knew all about the Morning War and had always been convinced that the quarians had brought that conflict on themselves. It seemed however, that the suited humanoids from Rannoch had found a way to cooperate with the Geth and there could only be one explanation to this fact "Yes, because the quarians resumed control"

"No, they did not" The Councilor replied sternly. "The Geth found a new purpose"

Nielsen narrowed his eyes with a venomous smile. _You don't really believe that, do you Councilor?_ "And what happens when their purpose is fulfilled? Can you assure me that they will not overrun the galaxy and turn us into their slaves?"

"They would have no reason to. The geth you remember are no longer the same" The Councilor confidently replied.

Nielsen bobbed his head and gave a small pout. He knew he was trying the Councilor's patience, but he had promised himself not to relent for even an instant. "I'm sorry to say I am not convinced Councilor. New AI without Shepard's control might very possibly turn hostile. What are we to do then with a fractured army on all sides?"

The Councilor cleared his throat before he answered and Nielsen knew he had hit the mark this time. "The armies are strengthening in numbers again, Nielsen. Granted there was not much need for soldiers during the long period of relative peace and many of them died in the war but when the Guardians left, the familiar groups started terrorizing the galaxy again and that has spurred on new talent"

Nielsen tried hard to suppress a chuckle at this attempt to produce an encouraging response. _He knows I'm right_. "Yes, I understand the Alliance is granting high ranks to inexperienced soldiers these days because they need officers. I wonder if that is the kind of army we want protecting our galaxy from synthetic abominations"

"I have no say in how the Alliance decides to promote its soldiers" replied the Councilor defensively. Dominic Osoba's blue eyes were rapidly filing with an intense hostility and Nielsen sensed that he ought to conclude his business quickly before he would indeed be refused audience in the future.

He rose from his chair and shot the Councilor a stern look. "We have tolerated the Geth because we were asked to by the Council, but I cannot promise that we will keep away from new abominations of this kind, Councilor. I only pray that the Council will remember the danger of artificial intelligence before it's too late"

He quickly turned and left the office, denying the Councilor a chance to respond, and released a heavy sigh as the doors to the office closed behind him. He headed in the direction of the elevator in his usual confident strides, but stopped in the lounge at the sudden buzzing of his omni-tool. He pushed the button and watched the familiar face of his assistant appear on the small holo-screen.

"Sir, I have just received word from one of our men in the Exodus Cluster" the assistant said, hesitation evident in his voice. Nielsen nodded and silently beckoned the young man continue. "A… A Guardian has been found on Eden Prime"

Nielsen immediately held his breath and stared at his assistant with wonder in his eyes. _My lord has returned!_

* * *

**Eden Prime, Exodus Cluster**

The M-60 Thunderbird hovered closer to the outline of the large mountain directly ahead and the Quinn gently pulled at the controls before she let her hand instinctively slide down over the cold metal of her side-arm. Before the mountain was a giant insect-like structure approximately 160 meters in length and seemingly intact, but missing its usual emissions of blue light between the large metallic plates. She stopped the Thunderbird a few meters from the Guardian and carefully exited, ignoring the inane chatter from her two fellow soldiers as they stepped out on the other side of the vehicle. She slowly drew her gun while she watched the reflections of moonlight on the surface of the Guardian and felt her upper lip start to perspire. _What the hell is this thing doing here?_

The ground beneath gave small cracks as she very slowly approached one of the arms of the Reaper, keeping her gaze fixed on the round holes that had served as the Guardians eyes and feeling her heartbeat increase rapidly with each tentative step. Her brow involuntarily furrowed with tenseness at the close proximity to this age-old enemy of the galaxy and she stole quick glances at her soldiers a few meters to her right. The expression of sheer awe on the face of her young Marine as he reached down to touch the Reaper made her immediately regret her decision to bring him along. _He has no idea. He was just a kid. _Her LC seemed less impressed even if she had been only seconds away from the annihilating blast of a Reaper destroyer in London before Shepard had then activated the Crucible and ordered the Reaper to cease fire. Quinn suspected however that Lieutenant-Commander Michaels was secretly hoping for the Guardian to come to life again and 'bring forth a new dawn of peace under the charitable eye of The Shepard' as she would say.

The Captain herself knew she was only waiting for the emissions to appear but not in the color of the harmless blue which had served as beacons of hope for so many people across the galaxy, but rather in the horrifying red such as she had seen as a young Corporal 9 years prior, before her CO had forcefully dragged her into a ruined building amidst the screams of terror from London residents in the street. _"We'll stay in here until it leaves" _Her CO's voice lingered in her head as an echo, drowning out all sounds around her as she felt the sheer and absolute panic, that had kept her frozen in a fetus-position in that building, slowly starting to take hold of her once again. There had been nothing but hoards of enemies outside and she and her CO had been the only survivors of a large platoon of 42 men and women. She had known that the building would hold no protection whatsoever from the devastating blasts of the Reapers and she had found no comfort in her CO's continuous attempts at keeping them both calm with random words of reassurance.

_"__it will all be over soon…"_

The roars and deafening noises from the street played repeatedly in her mind while she kept her armed hand fixed firmly in front of her. _Deep breaths now._ Random images of mangled bodies scattered around the rubble made a confusing collage in her mind and she blinked a few times in a fruitless attempt to keep herself focused before a sudden flash of green instantly brought her back to the present.

She turned her head and managed to catch a quick glimpse of the dumbfounded look on her LC's face before the woman keeled over against the patchy grass with a low groan of pain. The Captain parted her lips in complete astonishment. _What the… _

"Michaels? Lily?" She ran in long strides over to her fallen soldier and quickly kneeled down before her. Lieutenant-Commander Michaels eyes were wide and unresponsive and there was a steady cloud of froth emanating from her mouth. Quinn frantically wiped it away with a gloved hand and patted the LC on her cheeks repeatedly. "Michaels! Wake up!" No reply. "Lily, goddamnit, wake up!" Quinn shouted, but the LC remained paralyzed with a horrifying look of silent terror on her face. The Captain swallowed something and quickly beckoned her Marine closer to help her.

"What's happening to her?" asked the Marine in a horrified voice.

She looked up and met his brown eyes. _Fuck!_ "That thing is not dead!"


End file.
